Within the game's files is an unused graphic for an empty meter labeled "toxic". This was likely scrapped during development, though it's not clear what it would have been used for. Fans speculate that it would have served a purpose in a death mini game or time usage of the Freddy mask.

Two "shadow" animatronics exist in the game.

When looking in the "Parts and Service" room, occasionally the player can see "Shadow Freddy" sitting in the location where Bonnie starts. If the player stares at it for too long, the game will crash.

When putting down the monitor, the player will occasionally see what appears to be a "Shadow Bonnie". Like Shadow Freddy, if the player stares at it too long it will result in the game crashing. The only two ways to prevent the game from crashing are to put on the Freddy mask or pull up the monitor.

Just like in the original Five Nights at Freddy's, there is a poster in the office that will make a squeak noise when clicking Freddy's nose. This does not work in the mobile versions of the game.

On random occasions, the player can get the chance to play though an 8th night. This night gets rid of all the animatronics, with the exception of Foxy. This night is thought to be a bug as the game goes black if the player checks the cameras at anytime (with the only fix being to quit the game or let Foxy kill you) and if the player finishes the night, the game gets hung on the 6AM screen.

The melody of the Music Box was sampled from a Fisher Price Teaching Clock toy. The melody is from a song by Henry Clay Work called "My Grandfather's Clock".

If you fail to wind up the music box, before the Marionette kills you, there is a slight chance that an endoskeleton will be in the Prize Room, and/or the Left Vent.

The reason the animatronic The Puppet's difficulty cannot be altered in Night 7 is because its actions depend on what the player does throughout the game.

The plush toys found at the prize corner are the same plush toys that could be purchased in-game in the mobile version of the original Five Nights at Freddy's.

After completing the game, Spoiler:the player is rewarded with their end-game check with the money they've earned. The date on the check reads, "11/12/87", and the money earned is less than what the player receives in the first Five Nights at Freddy's. This suggests that the game is actually a prequel to the first game, and leads up to the events of the first game.